Difference between revisions of "Protocol-msud-task5 protocol"

From Bioinformatikpedia
(→‎HGMD)
(→‎HGMD)
Line 28: Line 28:
 
AGGTCAGCCTGTGGAACTTGCGCAGGTGCGAGTGGCCAGCAGAGGTCACGAATAAACTGCATCTCTGCGC
  
AGGTCAGCCTGTGGAACTTGCGCAGGTGCGAGTGGCCAGCAGAGGTCACGAATAAACTGCATCTCTGCGC
 
CTGGCTCTCTACCAAAAAAAAAAAAAAAAAA
  
CTGGCTCTCTACCAAAAAAAAAAAAAAAAAA
  +
= SNPdbe =
  +
  +
<table border=1>
  +
<tr><td>Mutation </td><td> Experimental evidence </td></tr>
  +
<tr><td>V3G</td><td>Not validated</td></tr>
  +
<tr><td>L17F</td><td>Not validated</td></tr>
  +
<tr><td>L17F</td><td>Not validated</td></tr>
  +
<tr><td>G29E</td><td>Not validated</td></tr>
  +
<tr><td>G29E</td><td>Not validated</td></tr>
  +
<tr><td>S36A</td><td>Not validated</td></tr>
  +
<tr><td>P39H</td><td>Not validated</td></tr>
  +
<tr><td>P39H</td><td>Not validated</td></tr>
  +
<tr><td>Q42R</td><td>Not validated</td></tr>
  +
<tr><td>Q42R</td><td>Not validated</td></tr>
  +
<tr><td>A59V</td><td>Not validated</td></tr>
  +
<tr><td>A59V</td><td>Not validated</td></tr>
  +
<tr><td>I62M</td><td>Not validated</td></tr>
  +
<tr><td>I62M</td><td>Not validated</td></tr>
  +
<tr><td>N71S</td><td>Not validated</td></tr>
  +
<tr><td>N71S</td><td>Not validated</td></tr>
  +
<tr><td>M82I</td><td>Not validated</td></tr>
  +
<tr><td>M82L</td><td>Not validated</td></tr>
  +
<tr><td>M82I</td><td>Not validated</td></tr>
  +
<tr><td>M82L</td><td>Not validated</td></tr>
  +
<tr><td>R117C</td><td>Not validated</td></tr>
  +
<tr><td>R117C</td><td>Not validated</td></tr>
  +
<tr><td>R127W</td><td>Not validated</td></tr>
  +
<tr><td>R127W</td><td>Not validated</td></tr>
  +
<tr><td>N150D</td><td>Not validated</td></tr>
  +
<tr><td>N150D</td><td>Not validated</td></tr>
  +
<tr><td>T151M</td><td>Not validated</td></tr>
  +
<tr><td>T151M</td><td>Not validated</td></tr>
  +
<tr><td>Q157A</td><td>Not validated</td></tr>
  +
<tr><td>Y158A</td><td>Not validated</td></tr>
  +
<tr><td>R159W</td><td>Not validated</td></tr>
  +
<tr><td>R159A</td><td>Not validated</td></tr>
  +
<tr><td>P170S</td><td>Not validated</td></tr>
  +
<tr><td>P170S</td><td>Not validated</td></tr>
  +
<tr><td>Q190K</td><td>Not validated</td></tr>
  +
<tr><td>R200C</td><td>Not validated</td></tr>
  +
<tr><td>R200C</td><td>Not validated</td></tr>
  +
<tr><td>S207A</td><td>Not validated</td></tr>
  +
<tr><td>L209A</td><td>Not validated</td></tr>
  +
<tr><td>T211A</td><td>Not validated</td></tr>
  +
<tr><td>T211M</td><td>Not validated</td></tr>
  +
<tr><td>A222T</td><td>Not validated</td></tr>
  +
<tr><td>A222T</td><td>Not validated</td></tr>
  +
<tr><td>E238A</td><td>Not validated</td></tr>
  +
<tr><td>G244R</td><td>Not validated</td></tr>
  +
<tr><td>G244R</td><td>Not validated</td></tr>
  +
<tr><td>A248D</td><td>Not validated</td></tr>
  +
<tr><td>G249S</td><td>Not validated</td></tr>
  +
<tr><td>G249S</td><td>Not validated</td></tr>
  +
<tr><td>A253T</td><td>Not validated</td></tr>
  +
<tr><td>A253T</td><td>Not validated</td></tr>
  +
<tr><td>A254D</td><td>Not validated</td></tr>
  +
<tr><td>C264W</td><td>Not validated</td></tr>
  +
<tr><td>C264W</td><td>Not validated</td></tr>
  +
<tr><td>R265W</td><td>Not validated</td></tr>
  +
<tr><td>R265W</td><td>Not validated</td></tr>
  +
<tr><td>R265K</td><td>Not validated</td></tr>
  +
<tr><td>R265A</td><td>Not validated</td></tr>
  +
<tr><td>N267S</td><td>Not validated</td></tr>
  +
<tr><td>Y269A</td><td>Not validated</td></tr>
  +
<tr><td>A285P</td><td>Not validated</td></tr>
  +
<tr><td>G289R</td><td>Not validated</td></tr>
  +
<tr><td>G290R</td><td>Not validated</td></tr>
  +
<tr><td>R296C</td><td>Not validated</td></tr>
  +
<tr><td>R297C</td><td>Not validated</td></tr>
  +
<tr><td>Y306H</td><td>Not validated</td></tr>
  +
<tr><td>Y307H</td><td>Not validated</td></tr>
  +
<tr><td>T309R</td><td>Not validated</td></tr>
  +
<tr><td>T310R</td><td>Not validated</td></tr>
  +
<tr><td>R313Q</td><td>Not validated</td></tr>
  +
<tr><td>R314Q</td><td>Not validated</td></tr>
  +
<tr><td>I326T</td><td>Not validated</td></tr>
  +
<tr><td>H336A</td><td>Not validated</td></tr>
  +
<tr><td>S337D</td><td>Not validated</td></tr>
  +
<tr><td>A343V</td><td>Not validated</td></tr>
  +
<tr><td>A344V</td><td>Not validated</td></tr>
  +
<tr><td>R345C</td><td>Not validated</td></tr>
  +
<tr><td>S346L</td><td>Not validated</td></tr>
  +
<tr><td>R346C</td><td>Not validated</td></tr>
  +
<tr><td>S347L</td><td>Not validated</td></tr>
  +
<tr><td>W354F</td><td>Not validated</td></tr>
  +
<tr><td>Q356R</td><td>Not validated</td></tr>
  +
<tr><td>Q357R</td><td>Not validated</td></tr>
  +
<tr><td>I360V</td><td>Not validated</td></tr>
  +
<tr><td>I361V</td><td>Not validated</td></tr>
  +
<tr><td>E397K</td><td>Not validated</td></tr>
  +
<tr><td>E398K</td><td>Not validated</td></tr>
  +
<tr><td>R398Q</td><td>Not validated</td></tr>
  +
<tr><td>R399Q</td><td>Not validated</td></tr>
  +
<tr><td>P402R</td><td>Not validated</td></tr>
  +
<tr><td>P403R</td><td>Not validated</td></tr>
  +
<tr><td>N403S</td><td>Not validated</td></tr>
  +
<tr><td>N404S</td><td>Not validated</td></tr>
  +
<tr><td>F408C</td><td>Not validated</td></tr>
  +
<tr><td>F409C</td><td>Not validated</td></tr>
  +
<tr><td>Y413C</td><td>Not validated</td></tr>
  +
<tr><td>Q423K</td><td>Not validated</td></tr>
  +
<tr><td>Q424K</td><td>Not validated</td></tr>
  +
<tr><td>R428H</td><td>Not validated</td></tr>
  +
<tr><td>R429H</td><td>Not validated</td></tr>
  +
<tr><td>Y437N</td><td>Not validated</td></tr>
  +
<tr><td>Y438N</td><td>Not validated</td></tr>
  +
</table>

Revision as of 14:38, 5 June 2012

HGMD

sequence used by HGMD can be found [here] 

>gi|38372929|ref|NM_000709.2| Homo sapiens branched chain keto acid dehydrogenase E1, alpha polypeptide (BCKDHA), mRNA
GCCGGACCGCTGAGTGGTTGTTAGCCAAGATGGCGGTAGCGATCGCTGCAGCGAGGGTCTGGCGGCTAAA
CCGTGGTTTGAGCCAGGCTGCCCTCCTGCTGCTGCGGCAGCCTGGGGCTCGGGGACTGGCTAGATCTCAC
CCCCCCAGGCAGCAGCAGCAGTTTTCATCTCTGGATGACAAGCCCCAGTTCCCAGGGGCCTCGGCGGAGT
TTATAGATAAGTTGGAATTCATCCAGCCCAACGTCATCTCTGGAATCCCCATCTACCGCGTCATGGACCG
GCAAGGCCAGATCATCAACCCCAGCGAGGACCCCCACCTGCCGAAGGAGAAGGTGCTGAAGCTCTACAAG
AGCATGACACTGCTTAACACCATGGACCGCATCCTCTATGAGTCTCAGCGGCAGGGCCGGATCTCCTTCT
ACATGACCAACTATGGTGAGGAGGGCACGCACGTGGGGAGTGCCGCCGCCCTGGACAACACGGACCTGGT
GTTTGGCCAGTACCGGGAGGCAGGTGTGCTGATGTATCGGGACTACCCCCTGGAACTATTCATGGCCCAG
TGCTATGGCAACATCAGTGACTTGGGCAAGGGGCGCCAGATGCCTGTCCACTACGGCTGCAAGGAACGCC
ACTTCGTCACTATCTCCTCTCCACTGGCCACGCAGATCCCTCAGGCGGTGGGGGCGGCGTACGCAGCCAA
GCGGGCCAATGCCAACAGGGTCGTCATCTGTTACTTCGGCGAGGGGGCAGCCAGTGAGGGGGACGCCCAT
GCCGGCTTCAACTTCGCTGCCACACTTGAGTGCCCCATCATCTTCTTCTGCCGGAACAATGGCTACGCCA
TCTCCACGCCCACCTCTGAGCAGTATCGCGGCGATGGCATTGCAGCACGAGGCCCCGGGTATGGCATCAT
GTCAATCCGCGTGGATGGTAATGATGTGTTTGCCGTATACAACGCCACAAAGGAGGCCCGACGGCGGGCT
GTGGCAGAGAACCAGCCCTTCCTCATCGAGGCCATGACCTACAGGATCGGGCACCACAGCACCAGTGACG
ACAGTTCAGCGTACCGCTCGGTGGATGAGGTCAATTACTGGGATAAACAGGACCACCCCATCTCCCGGCT
GCGGCACTATCTGCTGAGCCAAGGCTGGTGGGATGAGGAGCAGGAGAAGGCCTGGAGGAAGCAGTCCCGC
AGGAAGGTGATGGAGGCCTTTGAGCAGGCCGAGCGGAAGCCCAAACCCAACCCCAACCTACTCTTCTCAG
ACGTGTATCAGGAGATGCCCGCCCAGCTCCGCAAGCAGCAGGAGTCTCTGGCCCGCCACCTGCAGACCTA
CGGGGAGCACTACCCACTGGATCACTTCGATAAGTGAGACCTGCTCAGCCCACCCCCACCCATCCTCAGC
TACCCCGAGAGGTAGCCCCACTCTAAGGGGAGCAGGGGGACCTGACAGCACACCACTGTCTTCCCCAGTC
AGCTCCCTCTAAAATACTCAGCGGCCAGGGCGGCTGCCACTCTTCACCCCTGCTCCTCCCGGCTGTTACA
TTGTCAGGGGACAGCATCTGCAGCAGTTGCTGAGGCTCCGTCAGCCCCCTCTTCACCTGTTGTTACAGTG
CCTTCTCCCAGGGGCTGGGTGAGGGCACATTCAGGACTAGAAGCCCCTCTGGGCATGGGGTGGACATGGC
AGGTCAGCCTGTGGAACTTGCGCAGGTGCGAGTGGCCAGCAGAGGTCACGAATAAACTGCATCTCTGCGC
CTGGCTCTCTACCAAAAAAAAAAAAAAAAAA

SNPdbe

Mutation Experimental evidence
V3GNot validated
L17FNot validated
L17FNot validated
G29ENot validated
G29ENot validated
S36ANot validated
P39HNot validated
P39HNot validated
Q42RNot validated
Q42RNot validated
A59VNot validated
A59VNot validated
I62MNot validated
I62MNot validated
N71SNot validated
N71SNot validated
M82INot validated
M82LNot validated
M82INot validated
M82LNot validated
R117CNot validated
R117CNot validated
R127WNot validated
R127WNot validated
N150DNot validated
N150DNot validated
T151MNot validated
T151MNot validated
Q157ANot validated
Y158ANot validated
R159WNot validated
R159ANot validated
P170SNot validated
P170SNot validated
Q190KNot validated
R200CNot validated
R200CNot validated
S207ANot validated
L209ANot validated
T211ANot validated
T211MNot validated
A222TNot validated
A222TNot validated
E238ANot validated
G244RNot validated
G244RNot validated
A248DNot validated
G249SNot validated
G249SNot validated
A253TNot validated
A253TNot validated
A254DNot validated
C264WNot validated
C264WNot validated
R265WNot validated
R265WNot validated
R265KNot validated
R265ANot validated
N267SNot validated
Y269ANot validated
A285PNot validated
G289RNot validated
G290RNot validated
R296CNot validated
R297CNot validated
Y306HNot validated
Y307HNot validated
T309RNot validated
T310RNot validated
R313QNot validated
R314QNot validated
I326TNot validated
H336ANot validated
S337DNot validated
A343VNot validated
A344VNot validated
R345CNot validated
S346LNot validated
R346CNot validated
S347LNot validated
W354FNot validated
Q356RNot validated
Q357RNot validated
I360VNot validated
I361VNot validated
E397KNot validated
E398KNot validated
R398QNot validated
R399QNot validated
P402RNot validated
P403RNot validated
N403SNot validated
N404SNot validated
F408CNot validated
F409CNot validated
Y413CNot validated
Q423KNot validated
Q424KNot validated
R428HNot validated
R429HNot validated
Y437NNot validated
Y438NNot validated
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